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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN 5T4 (WNT-ACTIVATED INHIBITORY FACTOR 1, TROPHOBLAST GLYCOPROTEIN)
 
Authors :  Y. Zhao, T. Malinauskas, K. Harlos, E. Y. Jones
Date :  23 Jan 14  (Deposition) - 26 Feb 14  (Release) - 23 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Cell Adhesion, Waif1, Tpbg, Trovax, Mva-5T4, Cancer, Signaling, Leucine-Rich Repeats, Wnt/Beta-Catenin Signaling Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhao, T. Malinauskas, K. Harlos, E. Y. Jones
Structural Insights Into The Inhibition Of Wnt Signaling By Cancer Antigen 5T4/Wnt-Activated Inhibitory Factor 1.
Structure V. 22 612 2014
PubMed-ID: 24582434  |  Reference-DOI: 10.1016/J.STR.2014.01.009

(-) Compounds

Molecule 1 - TROPHOBLAST GLYCOPROTEIN
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Atcc Number: CRL-3022
    Expression System Cell Line: HEK293S GNTI-
    Expression System Common: HUMAN
    Expression System Plasmid: PURD-5T4/WAIF1ECTO
    Expression System Taxid: 9606
    Expression System Vector: PURD
    Expression System Vector Type: PLASMID
    Fragment: EXTRACELLULAR DOMAIN, RESIDUES 60-345
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 5T4 ONCOFETAL ANTIGEN, WNT-ACTIVATED INHIBITORY FACTOR, 5T4 ONCOFETAL TROPHOBLAST GLYCOPROTEIN, 5T4 ONCOTROPHOBLAST GLYCOPROTEIN, M6P1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PEG5Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:151 , ASN A:152 , PRO A:153 , HIS A:182 , ILE A:183 , VAL A:184BINDING SITE FOR RESIDUE PEG A1351
02AC2SOFTWAREGLU A:57 , THR A:58 , GLY A:59 , ASP A:60 , GLU A:67 , CYS A:68 , ASN A:338BINDING SITE FOR RESIDUE PEG A1352
03AC3SOFTWAREHIS A:182 , VAL A:184 , PRO A:185 , PRO A:186 , GLU A:189 , HIS A:221 , GLU A:327 , HOH A:2059 , HOH A:2060BINDING SITE FOR RESIDUE PEG A1353
04AC4SOFTWAREPHE A:138 , GLU A:139 , HIS A:140 , LEU A:141 , PRO A:142 , PRO A:174 , HOH A:2124BINDING SITE FOR RESIDUE PEG A1354
05AC5SOFTWAREALA A:303 , VAL A:306 , THR A:307 , LYS A:310 , SER A:339 , HOH A:2013 , HOH A:2113BINDING SITE FOR RESIDUE PEG A1355
06AC6SOFTWARESER A:126 , ASP A:148 , SER A:150 , HIS A:151 , ILE A:179 , ASN A:181 , GLU A:216 , NAG A:1345 , NAG A:1350BINDING SITE FOR RESIDUE CIT A1356
07AC7SOFTWAREASN A:79 , ARG A:80 , ASN A:81 , HIS A:238 , GLU A:261 , ARG A:288BINDING SITE FOR MONO-SACCHARIDE NAG A1347 BOUND TO ASN A 81
08AC8SOFTWARETHR A:99 , ASN A:124 , SER A:126 , ASP A:148 , ILE A:179 , CIT A:1356 , HOH A:2031BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1345 THROUGH NAG A1350 BOUND TO ASN A 124
09AC9SOFTWAREHIS A:182 , SER A:219 , HIS A:221 , ASN A:243 , HOH A:2059 , HOH A:2080BINDING SITE FOR MONO-SACCHARIDE NAG A1348 BOUND TO ASN A 243
10BC1SOFTWAREALA A:231 , ARG A:255 , ASN A:256 , GLU A:311 , THR A:312 , GLU A:313 , HOH A:2114BINDING SITE FOR MONO-SACCHARIDE NAG A1346 BOUND TO ASN A 256
11BC2SOFTWAREPRO A:234 , SER A:235 , ASN A:275 , ASP A:304BINDING SITE FOR MONO-SACCHARIDE NAG A1349 BOUND TO ASN A 275

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:62 -A:68
2A:66 -A:77
3A:298 -A:323
4A:300 -A:344

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:114 -Pro A:115
2Tyr A:325 -Pro A:326

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CNM)

(-) PROSITE Motifs  (1, 5)

Asymmetric/Biological Unit (1, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LRRPS51450 Leucine-rich repeat profile.TPBG_HUMAN92-113
143-164
235-256
211-232
259-280		  5A:92-113
A:143-164
A:235-256
A:211-232
A:259-280

(-) Exons   (0, 0)

(no "Exon" information available for 4CNM)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:283
 aligned with TPBG_HUMAN | Q13641 from UniProtKB/Swiss-Prot  Length:420

    Alignment length:288
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336        
           TPBG_HUMAN    57 PLPDQCPALCECSEAARTVKCVNRNLTEVPTDLPAYVRNLFLTGNQLAVLPAGAFARRPPLAELAALNLSGSRLDEVRAGAFEHLPSLRQLDLSHNPLADLSPFAFSGSNASVSAPSPLVELILNHIVPPEDERQNRSFEGMVVAALLAGRALQGLRRLELASNHFLYLPRDVLAQLPSLRHLDLSNNSLVSLTYVSFRNLTHLESLHLEDNALKVLHNGTLAELQGLPHIRVFLDNNPWVCDCHMADMVTWLKETEVVQGKDRLTCAYPEKMRNRVLLELNSADLDC 344
               SCOP domains d4cnma_ A: automated matches                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eee....eee..................eee......eee...............eee.....eeee............eee.......ee.........-----.....eee.......hhhhh..hhhhhhhhhhhhhhh.....eee.........hhhhhhhh....eee.....................eee.........hhhhhhhhh.....eee.....ee.hhhhhhhhhhhhhh..eehhhhh.eeehhhhh...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------LRR  PDB: A:92-113    -----------------------------LRR  PDB: A:143-164   ----------------------------------------------LRR  PDB: A:211-232   --LRR  PDB: A:235-256   --LRR  PDB: A:259-280   ---------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4cnm A  57 ETGDQCPALCECSEAARTVKCVNRNLTEVPTDLPAYVRNLFLTGNQLAVLPAGAFARRPPLAELAALNLSGSRLDEVRAGAFEHLPSLRQLDLSHNPLADLSPFAFSGSN-----PSPLVELILNHIVPPEDERQNRSFEGMVVAALLAGRALQGLRRLELASNHFLYLPRDVLAQLPSLRHLDLSNNSLVSLTYVSFRNLTHLESLHLEDNALKVLHNGTLAELQGLPHIRVFLDNNPWVCDCHMADMVTWLKETEVVQGKDRLTCAYPEKMRNRVLLELNSADLDC 344
                                    66        76        86        96       106       116       126       136       146       156       166     | 176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336        
                                                                                                                                       166   172
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CNM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CNM)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TPBG_HUMAN | Q13641)
biological process
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0051965    positive regulation of synapse assembly    Any process that activates, maintains or increases the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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        TPBG_HUMAN | Q13641: 4cnc

(-) Related Entries Specified in the PDB File

4cnc CRYSTAL STRUCTURE OF HUMAN 5T4 (WNT-ACTIVATED INHIBITORY FACTOR 1, TROPHOBLAST GLYCOPROTEIN)